Analysis of interatomic Contacts of Structural Units in PDB entry:
9YDA

Contacts of Structural Units (CSU) are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332).
This page provides analyses of contacts formed by:

chains
helices
sheets
residues

For analysis of ligand-protein contacts, use:

LPC software

3D structure can be seen in additional window with STING software for 9YDA entry

There are 5 chains in PDB entry 9YDA (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
R	ARG 37	LEU 336
B	ARG 8	ASN 340
G	ALA 7	ARG 62
H	ASP 18	LEU 264
A	CYS 3	PHE 350

There are 32 helices in PDB entry 9YDA. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	R	50	81	Right-handed alpha
Helix 2	AA2	R	82	85	Right-handed 310
Helix 3	AA3	R	86	88	Right-handed 310
Helix 4	AA4	R	89	115	Right-handed alpha
Helix 5	AA5	R	122	157	Right-handed alpha
Helix 6	AA6	R	165	184	Right-handed alpha
Helix 7	AA7	R	185	189	Right-handed 310
Helix 8	AA8	R	215	228	Right-handed alpha
Helix 9	AA9	R	228	251	Right-handed alpha
Helix 10	AB1	R	256	294	Right-handed alpha
Helix 11	AB2	R	302	304	Right-handed 310
Helix 12	AB3	R	305	312	Right-handed alpha
Helix 13	AB4	R	313	323	Right-handed alpha
Helix 14	AB5	R	326	334	Right-handed alpha
Helix 15	AB6	B	10	25	Right-handed alpha
Helix 16	AB7	G	8	23	Right-handed alpha
Helix 17	AB8	G	29	44	Right-handed alpha
Helix 18	AB9	G	45	48	Right-handed 310
Helix 19	AC1	G	55	59	Right-handed 310
Helix 20	AC2	H	91	93	Right-handed 310
Helix 21	AC3	H	104	108	Right-handed 310
Helix 22	AC4	H	237	241	Right-handed 310
Helix 23	AC5	A	6	32	Right-handed alpha
Helix 24	AC6	A	45	49	Right-handed 310
Helix 25	AC7	A	199	205	Right-handed 310
Helix 26	AC8	A	221	234	Right-handed alpha
Helix 27	AC9	A	235	239	Right-handed 310
Helix 28	AD1	A	249	260	Right-handed alpha
Helix 29	AD2	A	263	267	Right-handed 310
Helix 30	AD3	A	268	274	Right-handed 310
Helix 31	AD4	A	287	307	Right-handed alpha
Helix 32	AD5	A	326	347	Right-handed alpha

There are 14 sheets in PDB entry 9YDA. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8, AA9, AB1, AB2, AB3, AB4, AB5,

There are 2 strands in AA1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	R	194	196	first strand
Strand 2	R	203	205	anti-parallel

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There are 4 strands in AA2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	46	51	first strand
Strand 2	B	336	340	anti-parallel
Strand 3	B	327	331	anti-parallel
Strand 4	B	315	320	anti-parallel

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There are 4 strands in AA3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	58	63	first strand
Strand 2	B	69	74	anti-parallel
Strand 3	B	78	83	anti-parallel
Strand 4	B	88	94	anti-parallel

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There are 4 strands in AA4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	100	105	first strand
Strand 2	B	111	116	anti-parallel
Strand 3	B	121	125	anti-parallel
Strand 4	B	134	139	anti-parallel

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There are 4 strands in AA5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	146	153	first strand
Strand 2	B	156	161	anti-parallel
Strand 3	B	165	170	anti-parallel
Strand 4	B	175	181	anti-parallel

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There are 4 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	187	192	first strand
Strand 2	B	198	203	anti-parallel
Strand 3	B	208	212	anti-parallel
Strand 4	B	218	222	anti-parallel

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There are 4 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	229	234	first strand
Strand 2	B	240	245	anti-parallel
Strand 3	B	250	254	anti-parallel
Strand 4	B	259	264	anti-parallel

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There are 4 strands in AA8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	273	278	first strand
Strand 2	B	284	289	anti-parallel
Strand 3	B	294	298	anti-parallel
Strand 4	B	304	308	anti-parallel

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There are 4 strands in AA9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	20	24	first strand
Strand 2	H	35	42	anti-parallel
Strand 3	H	95	100	anti-parallel
Strand 4	H	85	90	anti-parallel

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There are 6 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	27	29	first strand
Strand 2	H	132	136	parallel
Strand 3	H	109	116	anti-parallel
Strand 4	H	50	56	anti-parallel
Strand 5	H	62	68	anti-parallel
Strand 6	H	75	77	anti-parallel

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There are 4 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	157	159	first strand
Strand 2	H	172	178	anti-parallel
Strand 3	H	228	233	anti-parallel
Strand 4	H	220	224	anti-parallel

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There are 5 strands in AB3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	163	165	first strand
Strand 2	H	260	263	parallel
Strand 3	H	243	248	anti-parallel
Strand 4	H	191	196	anti-parallel
Strand 5	H	203	206	anti-parallel

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There are 4 strands in AB4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	163	165	first strand
Strand 2	H	260	263	parallel
Strand 3	H	243	248	anti-parallel
Strand 4	H	255	256	anti-parallel

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There are 6 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	175	180	first strand
Strand 2	A	183	189	anti-parallel
Strand 3	A	33	40	parallel
Strand 4	A	209	215	parallel
Strand 5	A	242	248	parallel
Strand 6	A	315	319	parallel

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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il

Analysis of interatomic Contacts of Structural Units in PDB entry: 9YDA

Analysis of interatomic Contacts of Structural Units in PDB entry:
9YDA